rs5755495

Variant names:

• chr22-35002849-C-G
• rs5755495
• ENST00000668433.1:n.14G>C

Your query was ambiguous. Multiple possible variants found:

• chr22-35002849-C-G
• chr22-35002849-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000668433.1(LINC02885):​n.14G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,872 control chromosomes in the GnomAD database, including 29,311 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.61 (29309 hom., cov: 31)
  • Exomes 𝑓: 0.55 (2 hom.)
• Consequence: LINC02885 ENST00000668433.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

LINC02885 (HGNC:41188): (long intergenic non-protein coding RNA 2885)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02885	ENST00000668433.1	n.14G>C		non_coding_transcript_exon_variant	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93241 AN: 151730 Hom.: 29274 Cov.: 31

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.601

GnomAD4 exome AF: 0.545 AC: 12 AN: 22 Hom.: 2 Cov.: 0 AF XY: 0.550 AC XY: 11 AN XY: 20

Gnomad4 AMR exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.615 AC: 93335 AN: 151850 Hom.: 29309 Cov.: 31 AF XY: 0.619 AC XY: 45918 AN XY: 74204

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.688

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.606

Alfa AF: 0.591 Hom.: 3329

Bravo AF: 0.617

Asia WGS AF: 0.743 AC: 2584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.24
DANN	Benign	0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs5755495; hg19: chr22-35398839;